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Coexpression cluster:C230: Difference between revisions

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{{Coexpression_clusters
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adhesion!0.00609452779185376!8516;255743;54751;26032$GO:0007155!cell adhesion!0.00609452779185376!8516;255743;54751;26032$GO:0000902!cell morphogenesis!0.00933294408204043!8516;4856;54751$GO:0032989!cellular structure morphogenesis!0.00933294408204043!8516;4856;54751$GO:0030511!positive regulation of transforming growth factor beta receptor signaling pathway!0.0436562672371586!8516$GO:0032501!multicellular organismal process!0.0436562672371586!7871;8516;255743;51561;7068$GO:0005515!protein binding!0.0455961126751561!7871;8516;255743;4856;54751;51561;7068$GO:0009653!anatomical structure morphogenesis!0.0455961126751561!8516;4856;54751$GO:0004887!thyroid hormone receptor activity!0.0493564118487119!7068$GO:0007613!memory!0.0493564118487119!8516$GO:0005790!smooth endoplasmic 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,0.78794,0.61808,0.821636,0.877517,0.740239,0.273497,0.738682,0.0776308,0.752274,0.800664,0.308538,0.0897754,0.600398,0.75563,0.56878,0.532909,0.565097,0.495965,0.924757,0.911169,0.761157,0.203139,0.94675,0.556191,0.475458,0.274943,0.928319,0.707499,0.758554,0.243076,0.74629,0.0716473,0.690311,0.194912,0.0880718,0.382682,0.640271,0.686178,0.456917,0.875461,0.58579,0.710748,0.450754,0.145357,0.360889,0.241534,0.694126,0.496998,0.0169065,0.322714,0.0363305,0.155367,0.949685,0.871183,0.113061,0.885022,0.0937214,0.0274115,0.463163,0.0185717,0.198538,0.368,0.255351,0.358389,0.139663,0.548984,0.0788896,0.0496759,0.0124816|tfbs_overrepresentation_for_novel_motifs=0.0809908,0.0320858,0.167702,1.04942,0.113035,0.0912613,0.14804,0.020997,0.756107,0.391992,0.0728128,0.186739,0.349478,0.138529,0.36128,0.645125,0.38793,0.356808,0.948116,0.495899,0.72986,0.0195013,0.0862994,0.761994,0.114553,0.458041,0.511811,0.214768,0.803437,0.0419945,0.547251,0.859133,0.257308,0.500274,0.271361,0.110226,0.0737899,0.229701,0.701265,0.132609,0.267853,0.0528835,0.00370797,0.356919,0.225061,0.100632,0.971222,0.871565,0.468711,0.116833,0.484532,0.159064,0.699942,0.185058,0.285549,0.140925,0.387138,0.11539,0.297981,0.114647,0.164079,0.0384029,0.273657,0.109063,0.166587,0.311119,0.350587,0.658583,0.135992,0.516982,0.130295,0.109105,1.69906,0.775783,0.803452,0.113424,0.328023,0.101246,0.134296,0.037813,0.0116815,0.108558,0.673289,1.27577,0.248516,0.038236,5.78904,0.00230114,0.25041,0.748573,0.423767,0.230543,0.897689,1.33029,0.113904,0.0498762,0.178766,0.174731,0.255402,1.79195,0.116991,0.884666,0.171477,0.124329,0.0884977,0.183092,0.116504,0.580323,0.23996,0.320358,0.53239,0.169873,0.476835,0.389105,0.385616,0.823441,1.38664,3.47397,0.638073,0.0936256,0.27828,0.529765,0.224371,0.176466,1.19603,0.681385,0.0358539,0.466104,0.308831,0.320609,1.21831,0.0624214,2.34579,0.173424,0.434176,0.0316946,0.31276,0.215519,0.400154,1.17966,0.796831,0.370915,0.14418,0.51386,0.299676,0.495331,0.0822936,1.02612,0.490801,0.408953,0.0204391,0.899407,0.231247,0.152795,0.347598,0.543107,2.38417,0.0399858,0.0402511,0.193193,0.369974,0.219209,0.41716,0.35541,0.0962285,0.376624,0.362576,0.614907,0.00018331|tfbs_overrepresentation_jaspar=MA0003.1;0.00763123,MA0004.1;0.0758368,MA0006.1;0.0138739,MA0007.1;0.013777,MA0009.1;0.5904,MA0014.1;0.00473555,MA0017.1;0.712551,MA0019.1;0.425954,MA0024.1;0.142868,MA0025.1;1.45556,MA0027.1;1.65408,MA0028.1;0.00282582,MA0029.1;0.153483,MA0030.1;0.147145,MA0031.1;0.113758,MA0038.1;0.0382261,MA0040.1;0.923645,MA0041.1;0.687984,MA0042.1;2.07016,MA0043.1;0.590875,MA0046.1;0.574096,MA0048.1;0.446702,MA0050.1;0.353677,MA0051.1;0.962022,MA0052.1;5.36399,MA0055.1;0.0189582,MA0056.1;0,MA0057.1;0.211936,MA0058.1;0.0312766,MA0059.1;0.00558968,MA0060.1;0.00650561,MA0061.1;0.000675025,MA0063.1;0,MA0066.1;0.0383404,MA0067.1;0.43712,MA0068.1;0.100498,MA0069.1;0.195175,MA0070.1;0.188293,MA0071.1;0.52739,MA0072.1;0.545187,MA0073.1;0.0118851,MA0074.1;0.612568,MA0076.1;0.00696909,MA0077.1;0.180902,MA0078.1;0.889482,MA0081.1;0.564043,MA0083.1;0.209155,MA0084.1;0.596203,MA0087.1;0.541602,MA0088.1;0.0818829,MA0089.1;0,MA0090.1;0.67848,MA0091.1;0.637162,MA0092.1;0.52252,MA0093.1;0.114498,MA0095.1;0,MA0098.1;0,MA0100.1;0.162525,MA0101.1;0.0151805,MA0103.1;0.196461,MA0105.1;0.000323139,MA0106.1;0.187813,MA0107.1;0.000581946,MA0108.2;0.112274,MA0109.1;0,MA0111.1;1.03616,MA0113.1;0.448904,MA0114.1;0.0962767,MA0115.1;0.376065,MA0116.1;0.67173,MA0117.1;0.22866,MA0119.1;0.316526,MA0122.1;0.688133,MA0124.1;0.344064,MA0125.1;0.282149,MA0130.1;0,MA0131.1;0.0757356,MA0132.1;0,MA0133.1;0,MA0135.1;0.223906,MA0136.1;0.0401427,MA0139.1;0.670025,MA0140.1;0.52088,MA0141.1;1.45535,MA0142.1;0.325628,MA0143.1;1.67279,MA0144.1;0.0352477,MA0145.1;0.0251939,MA0146.1;1.54168e-05,MA0147.1;0.0196811,MA0148.1;0.708648,MA0149.1;0.0260116,MA0062.2;0.00057408,MA0035.2;0.116515,MA0039.2;3.12474e-06,MA0138.2;0.0692079,MA0002.2;0.0158277,MA0137.2;0.00312686,MA0104.2;0.00639385,MA0047.2;0.703125,MA0112.2;0.00991655,MA0065.2;0.00680845,MA0150.1;0.115109,MA0151.1;0,MA0152.1;0.291292,MA0153.1;0.744058,MA0154.1;0.412933,MA0155.1;0.00759935,MA0156.1;0.00323821,MA0157.1;0.0868108,MA0158.1;0,MA0159.1;0.205404,MA0160.1;0.758995,MA0161.1;0,MA0162.1;2.99606e-05,MA0163.1;2.5869e-05,MA0164.1;0.216326,MA0080.2;0.0483055,MA0018.2;0.189138,MA0099.2;0.537899,MA0079.2;7.15049e-14,MA0102.2;0.629093,MA0258.1;0.0102397,MA0259.1;0.0594418,MA0442.1;0}}
|full_id=C230_aorta_normal_heart_penis_osteosarcoma_basal_lung
|id=C230
}}

Latest revision as of 11:01, 17 September 2013


Full id: C230_aorta_normal_heart_penis_osteosarcoma_basal_lung



Phase1 CAGE Peaks

Hg19::chr10:15646574..15646578,-p11@ITGA8
Hg19::chr10:15760797..15760808,-p@chr10:15760797..15760808
-
Hg19::chr10:15760828..15760842,-p@chr10:15760828..15760842
-
Hg19::chr10:15761845..15761856,-p4@ITGA8
Hg19::chr10:15761884..15761936,-p1@ITGA8
Hg19::chr10:15761954..15761965,-p7@ITGA8
Hg19::chr10:15761966..15761979,-p2@ITGA8
Hg19::chr10:15762207..15762225,-p8@ITGA8
Hg19::chr10:15762227..15762257,-p3@ITGA8
Hg19::chr10:15762274..15762283,-p12@ITGA8
Hg19::chr10:15762312..15762340,-p6@ITGA8
Hg19::chr10:15762346..15762358,-p9@ITGA8
Hg19::chr12:19928351..19928358,+p2@ENST00000535764
Hg19::chr12:19928380..19928401,+p1@ENST00000535764
Hg19::chr13:39952800..39952810,-p@chr13:39952800..39952810
-
Hg19::chr14:92307575..92307589,-p@chr14:92307575..92307589
-
Hg19::chr14:92307596..92307610,-p@chr14:92307596..92307610
-
Hg19::chr14:92307628..92307643,-p@chr14:92307628..92307643
-
Hg19::chr16:2173505..2173521,-p1@AF088750
Hg19::chr16:73127519..73127528,-p@chr16:73127519..73127528
-
Hg19::chr16:73127560..73127571,-p@chr16:73127560..73127571
-
Hg19::chr17:12570155..12570163,+p@chr17:12570155..12570163
+
Hg19::chr1:16084107..16084112,+p19@FBLIM1
Hg19::chr1:163117077..163117096,-p@chr1:163117077..163117096
-
Hg19::chr1:48224242..48224244,+p@chr1:48224242..48224244
+
Hg19::chr22:25466244..25466263,+p8@KIAA1671
Hg19::chr22:25466273..25466284,+p7@KIAA1671
Hg19::chr22:25466305..25466317,+p6@KIAA1671
Hg19::chr2:107467431..107467465,-p@chr2:107467431..107467465
-
Hg19::chr2:18116344..18116353,+p@chr2:18116344..18116353
+
Hg19::chr2:285923..285935,+p1@ENST00000450709
Hg19::chr2:28958958..28958989,-p1@ENST00000444501
Hg19::chr2:28959059..28959099,-p1@ENST00000452212
Hg19::chr2:33285212..33285215,+p@chr2:33285212..33285215
+
Hg19::chr2:33285233..33285259,+p@chr2:33285233..33285259
+
Hg19::chr2:33285264..33285274,+p@chr2:33285264..33285274
+
Hg19::chr3:24231794..24231799,-p38@THRB
Hg19::chr3:29966392..29966406,+p22@RBMS3
Hg19::chr3:33260352..33260365,-p3@SUSD5
Hg19::chr3:33260373..33260422,-p2@SUSD5
Hg19::chr3:33260478..33260490,-p8@SUSD5
Hg19::chr3:33260765..33260770,-p7@SUSD5
Hg19::chr3:57881966..57881977,+p13@SLMAP
Hg19::chr3:57882024..57882045,+p10@SLMAP
Hg19::chr3:57882061..57882085,+p4@SLMAP
Hg19::chr4:106833328..106833353,+p7@NPNT
Hg19::chr4:119860470..119860487,+p@chr4:119860470..119860487
+
Hg19::chr4:15429533..15429568,-p1@ENST00000502344
Hg19::chr4:174846835..174846846,+p@chr4:174846835..174846846
+
Hg19::chr5:122448503..122448506,+p@chr5:122448503..122448506
+
Hg19::chr5:59792105..59792117,-p@chr5:59792105..59792117
-
Hg19::chr6:84743412..84743431,+p2@MRAP2
Hg19::chr6:84743436..84743496,+p1@MRAP2
Hg19::chr7:40549076..40549087,+p@chr7:40549076..40549087
+
Hg19::chr7:40549088..40549102,+p@chr7:40549088..40549102
+
Hg19::chr7:73462921..73462932,+p@chr7:73462921..73462932
+
Hg19::chr7:73468280..73468302,-p@chr7:73468280..73468302
-
Hg19::chr8:120428678..120428695,+p1@NOV
Hg19::chr8:120430391..120430409,+p@chr8:120430391..120430409
+
Hg19::chr8:120435183..120435195,-p1@CU677182
Hg19::chr8:97398865..97398877,-p1@ENST00000523862


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0022610biological adhesion0.00609452779185376
GO:0007155cell adhesion0.00609452779185376
GO:0000902cell morphogenesis0.00933294408204043
GO:0032989cellular structure morphogenesis0.00933294408204043
GO:0030511positive regulation of transforming growth factor beta receptor signaling pathway0.0436562672371586
GO:0032501multicellular organismal process0.0436562672371586
GO:0005515protein binding0.0455961126751561
GO:0009653anatomical structure morphogenesis0.0455961126751561
GO:0004887thyroid hormone receptor activity0.0493564118487119
GO:0007613memory0.0493564118487119
GO:0005790smooth endoplasmic reticulum0.0493564118487119



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism3.12e-37114
meninx2.02e-122
membrane organ2.02e-122
meningeal cluster2.02e-122
valve9.70e-093
cardiac mesenchyme9.70e-093
cardial valve9.70e-093
tunica intima9.70e-093
heart layer9.70e-093
endocardium9.70e-093
endocardial cushion9.70e-093
presumptive endocardium9.70e-093
pulmonary valve3.13e-071
semi-lunar valve3.13e-071
penis3.32e-071
intromittent organ3.32e-071
lateral plate mesenchyme3.32e-071
undifferentiated genital tubercle3.32e-071
somatopleure3.32e-071
mitral valve3.95e-071
dura mater4.18e-071
future meninx4.18e-071
ectomeninx4.18e-071
future dura mater4.18e-071
uterus or analog4.69e-071
epididymis6.99e-071


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.00763123
MA0004.10.0758368
MA0006.10.0138739
MA0007.10.013777
MA0009.10.5904
MA0014.10.00473555
MA0017.10.712551
MA0019.10.425954
MA0024.10.142868
MA0025.11.45556
MA0027.11.65408
MA0028.10.00282582
MA0029.10.153483
MA0030.10.147145
MA0031.10.113758
MA0038.10.0382261
MA0040.10.923645
MA0041.10.687984
MA0042.12.07016
MA0043.10.590875
MA0046.10.574096
MA0048.10.446702
MA0050.10.353677
MA0051.10.962022
MA0052.15.36399
MA0055.10.0189582
MA0056.10
MA0057.10.211936
MA0058.10.0312766
MA0059.10.00558968
MA0060.10.00650561
MA0061.10.000675025
MA0063.10
MA0066.10.0383404
MA0067.10.43712
MA0068.10.100498
MA0069.10.195175
MA0070.10.188293
MA0071.10.52739
MA0072.10.545187
MA0073.10.0118851
MA0074.10.612568
MA0076.10.00696909
MA0077.10.180902
MA0078.10.889482
MA0081.10.564043
MA0083.10.209155
MA0084.10.596203
MA0087.10.541602
MA0088.10.0818829
MA0089.10
MA0090.10.67848
MA0091.10.637162
MA0092.10.52252
MA0093.10.114498
MA0095.10
MA0098.10
MA0100.10.162525
MA0101.10.0151805
MA0103.10.196461
MA0105.10.000323139
MA0106.10.187813
MA0107.10.000581946
MA0108.20.112274
MA0109.10
MA0111.11.03616
MA0113.10.448904
MA0114.10.0962767
MA0115.10.376065
MA0116.10.67173
MA0117.10.22866
MA0119.10.316526
MA0122.10.688133
MA0124.10.344064
MA0125.10.282149
MA0130.10
MA0131.10.0757356
MA0132.10
MA0133.10
MA0135.10.223906
MA0136.10.0401427
MA0139.10.670025
MA0140.10.52088
MA0141.11.45535
MA0142.10.325628
MA0143.11.67279
MA0144.10.0352477
MA0145.10.0251939
MA0146.11.54168e-05
MA0147.10.0196811
MA0148.10.708648
MA0149.10.0260116
MA0062.20.00057408
MA0035.20.116515
MA0039.23.12474e-06
MA0138.20.0692079
MA0002.20.0158277
MA0137.20.00312686
MA0104.20.00639385
MA0047.20.703125
MA0112.20.00991655
MA0065.20.00680845
MA0150.10.115109
MA0151.10
MA0152.10.291292
MA0153.10.744058
MA0154.10.412933
MA0155.10.00759935
MA0156.10.00323821
MA0157.10.0868108
MA0158.10
MA0159.10.205404
MA0160.10.758995
MA0161.10
MA0162.12.99606e-05
MA0163.12.5869e-05
MA0164.10.216326
MA0080.20.0483055
MA0018.20.189138
MA0099.20.537899
MA0079.27.15049e-14
MA0102.20.629093
MA0258.10.0102397
MA0259.10.0594418
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
RAD21#5885122.037055848286490.01280435981619930.0460700222153181



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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